Genotyping-by-sequencing of a bi-parental mapping population segregating for downy mildew resistance in hop (Humulus lupulus L.)

Henning, Jimmy C.; Gent, David H.; Twomey, Megan C.; Townsend, M. Shaun; Pitra, Nicholi J.; Matthews, Paul D.

doi:10.1007/s10681-015-1600-3

Cited by 20 publications

(29 citation statements)

References 33 publications

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“…Zhang et al (2018a) used a four-way RIL to perform GWAS on the genetic mechanism of soybean protein. Henning et al (2016) conducted GWAS using a hop population constructed from the parents "Teamaker" and USDA 21422M, revealing the genetic basis of fiber quality traits and yield components in 231 lines. Liu et al (2018) used a F 6:8 RIL derived from cotton cultivars " Lumianyan28" and "Xinluzao24" to detect 134 QTLs for fiber quality traits and 122 QTLs for yield components, with 35 common candidate genes.…”

Section: Introductionmentioning

confidence: 99%

Linkage Analysis and Multi-Locus Genome-Wide Association Studies Identify QTNs Controlling Soybean Plant Height

et al. 2020

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Plant height is an important target for soybean breeding. It is a typical quantitative trait controlled by multiple genes and is susceptible to environmental influences. Here, we carried out phenotypic analysis of 156 recombinant inbred lines derived from "Dongnong L13" and "Henong 60" in nine environments at four locations over 6 years using interval mapping and inclusive composite interval mapping methods. We performed quantitative trait locus (QTL) analysis by applying pre-built simple-sequence repeat maps. We detected 48 QTLs, including nine significant QTLs detected by multiple methods and in multiple environments. Meanwhile, genotyping of all lines using the SoySNP660k BeadChip produced 54,836 non-redundant single-nucleotide polymorphism (SNP) genotypes. We used five multi-locus genome-wide association analysis methods to locate 10 quantitative trait nucleotides (QTNs), four of which overlap with previously located QTLs. Five candidate genes related to plant height are predicted to lie within 200 kb of these four QTNs. We identified 19 homologous genes in Arabidopsis, two of which may be associated with plant height. These findings further our understanding of the multigene regulatory network and genetic determinants of soybean plant height, which will be important for breeding high-yielding soybean.

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Section: Introductionmentioning

confidence: 99%

Linkage Analysis and Multi-Locus Genome-Wide Association Studies Identify QTNs Controlling Soybean Plant Height

et al. 2020

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“…This study utilized phenotyping and raw sequence data from Henning et al (2017) and as such represents a limited evaluation of individuals for a genetic mapping and QTL study. Nevertheless, the sequencing depth for all individuals (48 individual genotypes per Illumina HiSeq 3000 sequencing lane) that were genotyped-by-sequencing was relatively high in comparison to previous GBS studies (Henning et al 2016).…”

Section: Discussionmentioning

confidence: 82%

“…All plant materials (parents and offspring) for DNA samples were grown under glasshouse conditions with all attempts to control pathogen and insect infestation as described by Henning et al (2017). A modified extraction protocol using Qiagen DNAeasy Mini extraction kits (QIagen Incorporated, Germantown, MD) was used to extract DNA from young hop leaves as described by Henning et al (2016). Genotyping-bysequencing was performed as described by Elshire et al (2011) using an Illumina HiSeq 3000 sequencing.…”

Section: Genotyping-by-sequencing Qtl Analysis and Association Studiesmentioning

confidence: 99%

Genomic analysis of powdery mildew resistance in a hop (Humulus lupulus L.) bi-parental population segregating for “R6-locus”

2019

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Genetic response in hop to fungal pathogen infection has been evaluated at the chromosomal level through QTL analyses but very little information exists on the expression of genes during infection periods. Raw GBS reads and phenotypic data from a previously published QTL analysis along with a newly assembled PacBio-derived hop reference genome were used to re-evaluate resistance to races v4/v6 of powdery mildew (PM; Podosphaera humuli). QTL analyses revealed two tightly linked regions of association on a single linkage group. The three SNP markers most tightly linked to PM resistance (found on contig 000559F) were observed downstream from a putative R-gene locus for powdery mildew resistance. This 230 kb region contained a series of seven putative R-genes surrounded by seven putative peroxidase-3 genes downstream and seven putative glucan endo-1,3-beta-glucosidase upstream and an expressed F-box domain protein. RNAseq data showed all putative R-genes along with all putative glucan endo-1,3-beta-glucosidase genes were expressed under diseased conditions, while none of the peroxidase genes were expressed. The second region contained three SNPs found on contig 002916F next to two putative R-genes. RNAseq data showed complex expression of exons contained in putative isoforms of R-genes. This preliminary information will prove valuable information for development of precise markers located either within or next to genes responsible for race v4/v6 PM resistance.

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“…This study utilized phenotyping and raw sequence data from Henning et al (2017) and as such represents a limited evaluation of individuals for a genetic mapping and QTL study. Nevertheless, the sequencing depth for all individuals (48 individual genotypes per Illumina HiSeq 3000 sequencing lane) that were genotyped-bysequencing was relatively high in comparison to previous GBS studies (Henning et al, 2016). In addition, the use of controlled environmental conditions in a glasshouse along with controlled inoculations resulted in consistent phenotypic values across replications.…”

Section: Discussionmentioning

confidence: 86%

“…All plant materials (parents and offspring) for DNA samples were grown under glasshouse conditions with all attempts to control pathogen and insect infestation as described by Henning et al (2017). A modified extraction protocol using Qiagen DNAeasy Mini extraction kits (QIagen Incorporated, Germantown, MD) was used to extract DNA from young hop leaves as described by Henning et al (2016). Genotyping-by-sequencing was performed as described by Elshire et al (2011) using an Illumina HiSeq 3000 sequencing.…”

Section: Genotyping-by-sequencing Qtl Analysis and Association Studiesmentioning

confidence: 99%

Genomic Analysis of Powdery Mildew Resistance in a Hop (Humulus lupulusL.) Bi-parental Population Segregating for “R6-locus”

Padgitt-Cobb

Kingan

Henning

2019

Preprint

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Genetic response in hop to fungal pathogen infection has been evaluated at the chromosomal level through QTL analyses but very little information exists on the expression of genes during infection periods. Raw GBS reads and phenotypic data from a previously published QTL analysis along with a newly assembled PacBioderived hop reference genome were used to re-evaluate resistance to races v4/v6 of powdery mildew (PM; Podosphaera humuli). QTL analyses revealed two tightly linked regions of association on a single linkage group. The three SNP markers most tightly linked to PM resistance (found on contig 000559F) were observed downstream from a putative R-gene locus for powdery mildew resistance. This 230 kb region contained a series of seven putative R-genes surrounded by seven putative peroxidase-3 genes downstream and seven putative glucan endo-1,3-betaglucosidase upstream and an expressed F-box domain protein. RNAseq data showed all putative R-genes along with all putative glucan endo-1,3-betaglucosidase genes were expressed under diseased conditions, while none of the peroxidase genes were expressed. The second region contained three SNPs found on contig 002916F next to two putative R-genes. RNAseq data showed complex expression of exons contained in putative isoforms of R-genes. This preliminary information will prove valuable information for development of precise markers located either within or next to genes responsible for race v4/v6 PM resistance.

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Genotyping-by-sequencing of a bi-parental mapping population segregating for downy mildew resistance in hop (Humulus lupulus L.)

Cited by 20 publications

References 33 publications

Linkage Analysis and Multi-Locus Genome-Wide Association Studies Identify QTNs Controlling Soybean Plant Height

Linkage Analysis and Multi-Locus Genome-Wide Association Studies Identify QTNs Controlling Soybean Plant Height

Genomic analysis of powdery mildew resistance in a hop (Humulus lupulus L.) bi-parental population segregating for “R6-locus”

Genomic Analysis of Powdery Mildew Resistance in a Hop (Humulus lupulusL.) Bi-parental Population Segregating for “R6-locus”

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